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| Status |
Public on Apr 24, 2020 |
| Title |
E12.0PG_ATACseq_rep3 |
| Sample type |
SRA |
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| Source name |
Organ of Corti
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| Organism |
Mus musculus |
| Characteristics |
cell type: Organ of Corti progenitor cells (Sox2-GFP+)
age: E12.0
antibody: NA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Progenitors (Sox2-GFP+) were purified from E12 cochlea by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were amplified by PCR with indexed primers.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
The quality of the libraries was confirmed using a Bioanalyzer (Quick Biology Inc.). Reads were mapped to GRCm38/mm10 genome assembly using STAR.
For RNAseq, genes.results files provided for each sample contain length, effective length, and expected counts for each gene.
For ATAC and CUTnRUN libraries, Endcode pipeline was used; PCR duplicates were removed based on genomic coordinates for ATAC-seq, or by MIDs using UMI-tools for CUT&RUN.
Peaks were called by Model-based analysis of ChIP-Seq (MACS2) with FDR< 0.01 and the dynamic lambda (--nolambda) option for individual replicates.
NarrowPeak files provide the list of called peaks of significant signal enrichment.
Genome_build: GRCm38/mm10 genome
Supplementary_files_format_and_content: *.genes.results.txt
Supplementary_files_format_and_content: *.narrowPeak
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| Submission date |
Apr 23, 2020 |
| Last update date |
Apr 24, 2020 |
| Contact name |
Neil Segil |
| E-mail(s) |
nsegil@med.usc.edu
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| Phone |
3234421549
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| Organization name |
University of Southern California
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| Department |
BCC
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| Lab |
503K
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| Street address |
1425 san pablo st, BCC 503K
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE149254 |
Organ of Corti size is governed by Yap/Tead-mediated progenitor self-renewal |
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| Relations |
| BioSample |
SAMN14682312 |
| SRA |
SRX8167855 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4494958_E12.0PG_ATACseq_rep3.narrowPeak.gz |
1.7 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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